1D9S

TUMOR SUPPRESSOR P15(INK4B) STRUCTURE BY COMPARATIVE MODELING AND NMR DATA


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
13D_15N-SEPARATED_NOESY0.2 MM P15, U-15N; 4 MM HEPES, 1 MM DTT, 5 UM EDTA95% H2O/5% D2O0.17.5AMBIENT293
2HNCA0.2 MM P15, U-15N,13C; 4 MM HEPES, 1 MM DTT, 5 UM EDTA95% H2O/5% D2O0.17.5AMBIENT293
3CBCA(CO)NH0.2 MM P15, U-15N,13C; 4 MM HEPES, 1 MM DTT, 5 UM EDTA95% H2O/5% D2O0.17.5AMBIENT293
43D_13C-SEPARATED_NOESY0.2 MM P15, U-15N,13C; 4 MM HEPES, 1 MM DTT, 5 UM EDTA100% D2O0.17.5AMBIENT293
53D_13C-SEPARATED_TOCSY0.2 MM P15, U-15N,13C; 4 MM HEPES, 1 MM DTT, 5 UM EDTA100% D2O0.17.5AMBIENT293
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerDRX800
2BrukerDMX600
NMR Refinement
MethodDetailsSoftware
COMPARATIVE MODELING, RESTRAINT ENERGY MINIMIZATIONDUE TO THE STRUCTURAL FLEXIBILITY AND INSTABILITY OF P15, ONLY A LIMITED NUMBER OF NMR CONSTRAINTS WERE COLLECTED. BECAUSE P15 SHARES MORE THAN 85% SEQUENCE HOMOLOGY WITH P16, 19 P15 STRUCTURES WERE GENERATED BY USING COMPARATIVE MODELING (MODELLER-4) WITH AN ENSEMBLE OF P16(INK4A) NMR STRUCTURES AS TEMPLATES. THE MODELING STRUCTURES WERE THEN SUBJECTED TO 1400 STEPS OF RESTRAINT ENERGY MINIMIZATION (X-PLOR) WITH THE NMR DATA (672 DISTANCE CONSTRAINTS). THE STRUCTURES THAT SATISFY THE NMR CONSTRAINTS WERE PICKED TO REPRESENT P15(INK4B).XwinNMR
NMR Ensemble Information
Conformer Selection CriteriaSTRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY
Conformers Calculated Total Number19
Conformers Submitted Total Number10
Representative Model10 (minimized average structure)
Additional NMR Experimental Information
DetailsTRIPLE-RESONANCE NMR SPECTROSCOPY WAS USED TO DETERMINE THE P15 STRUCTURE
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionXwinNMR2.1BRUKER
2refinementX-PLOR3.1BRUNGER
3structure solutionMODELLER-44.0SALI